Contacts of the helix formed by residues 703 - 719 (chain A) in PDB entry 6X70
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 703 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 4.5 0.9 - - - -
701A THR* 3.0 20.9 + - - +
702A ASN* 1.3 82.9 - - - +
704A PHE* 1.3 65.8 + - - +
705A GLY* 4.5 2.2 - - - +
706A ILE* 3.2 25.6 + - + +
707A ILE* 3.1 24.9 + - - +
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Residues in contact with PHE 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A GLU* 3.5 47.1 - - + -
647A CYS* 4.2 3.4 - - + -
648A GLN* 4.2 14.6 - - + -
651A LEU* 3.7 25.6 - - + -
702A ASN 3.5 4.6 + - - -
703A GLU* 1.3 71.0 - - - +
705A GLY* 1.3 65.0 + - - +
707A ILE 4.6 0.2 - - - +
708A ALA* 2.8 60.0 + - + +
712A LYS* 5.9 0.7 - - - -
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Residues in contact with GLY 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A GLU* 3.2 3.2 - - - +
704A PHE* 1.3 86.3 - - - +
706A ILE* 1.3 64.3 + - - +
708A ALA* 5.2 0.4 - - - -
709A THR* 2.5 30.6 + - - -
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Residues in contact with ILE 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A LEU* 4.7 17.3 - - + -
701A THR* 4.1 22.4 - - + +
703A GLU* 3.2 30.8 + - + +
704A PHE 3.1 0.4 - - - -
705A GLY* 1.3 82.0 - - - +
707A ILE* 1.3 67.2 + - - +
709A THR* 3.9 1.7 - - - -
710A GLU* 3.1 23.4 + - + +
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Residues in contact with ILE 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A CYS* 4.3 13.0 - - + -
651A LEU* 3.9 24.2 - - + -
661A THR* 3.7 25.8 - - + -
664A ILE* 3.9 14.3 - - + +
697A LEU* 4.0 20.6 - - + -
701A THR* 3.9 15.9 - - + +
702A ASN 4.2 1.3 - - - -
703A GLU 3.1 16.7 + - - +
704A PHE* 4.4 2.2 - - - +
706A ILE* 1.3 76.6 - - - +
708A ALA* 1.3 59.7 + - - +
710A GLU* 3.2 2.3 + - - +
711A MET* 2.8 30.1 + - + +
732A PHE* 3.6 29.8 - - + -
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Residues in contact with ALA 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A ILE* 4.6 0.6 - - + +
644A GLU* 4.6 10.3 - - + -
647A CYS* 3.9 18.1 - - - +
704A PHE* 2.8 58.2 + - + +
705A GLY* 4.9 0.4 - - - +
707A ILE* 1.3 73.0 - - - +
709A THR* 1.3 56.3 + - - +
711A MET* 3.2 1.9 + - - +
712A LYS* 2.9 38.0 + - - +
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Residues in contact with THR 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A GLY* 2.5 27.2 + - - -
706A ILE* 3.5 3.3 + - - -
707A ILE 3.3 0.4 - - - -
708A ALA* 1.3 78.7 - - - +
710A GLU* 1.3 57.8 + - - +
712A LYS* 3.3 14.2 + - - +
713A SER* 2.9 29.0 + - - -
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Residues in contact with GLU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ILE* 3.7 21.1 - - + -
693A ARG* 5.4 0.7 + - - -
695A SER* 3.2 33.7 + - - +
697A LEU* 4.3 9.6 - - + -
706A ILE* 3.1 18.1 + - + +
709A THR* 1.3 76.1 - - - +
711A MET* 1.3 52.4 + - - +
713A SER* 3.1 15.0 + - - -
714A LEU* 2.7 48.8 + - + +
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Residues in contact with MET 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ILE* 3.8 18.4 - - + -
647A CYS* 3.8 13.9 - - - -
664A ILE* 3.8 20.0 - - + -
665A THR 3.2 33.9 - - - +
666A LEU* 3.7 15.6 - - - +
707A ILE* 2.8 20.6 + - + +
708A ALA 3.6 4.3 - - - +
710A GLU* 1.3 76.7 - - - +
712A LYS* 1.3 62.1 + - - +
714A LEU* 3.2 7.1 + - - +
715A TYR 3.0 17.7 + - - -
730A LEU* 3.8 23.6 - - + -
731A GLN 3.6 24.5 - - - +
732A PHE* 4.2 12.1 - - + -
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Residues in contact with LYS 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A ASP* 3.4 40.5 + - + +
643A ILE* 3.8 22.7 - - + -
644A GLU* 2.5 40.2 + - + +
704A PHE* 5.9 0.8 - - - -
708A ALA* 2.9 28.2 + - - +
709A THR* 3.9 10.4 + - - +
711A MET* 1.3 74.9 - - - +
713A SER* 1.3 61.9 + - - +
715A TYR* 3.3 2.8 + - - +
716A ARG* 3.2 40.7 + - - +
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Residues in contact with SER 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A THR* 2.9 15.4 + - - -
710A GLU* 3.1 24.7 + - - -
712A LYS* 1.3 73.9 - - - +
714A LEU* 1.3 66.6 + - - +
716A ARG* 3.1 12.2 + - - +
717A THR* 3.1 29.6 + - - +
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Residues in contact with LEU 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ILE* 4.1 28.5 - - + +
666A LEU* 3.9 23.8 - - + +
693A ARG* 3.4 55.4 - - + +
694A SER 4.1 0.9 - - - +
695A SER* 4.1 12.3 - - - -
710A GLU* 2.7 36.0 + - - +
711A MET* 3.2 13.2 + - - +
713A SER* 1.3 71.5 - - - +
715A TYR* 1.3 64.2 + - - +
717A THR* 2.7 23.2 + - + -
718A LEU* 3.3 8.7 + - - +
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Residues in contact with TYR 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A ILE* 3.6 28.9 - - + -
639A VAL* 3.7 23.1 - - + +
643A ILE* 4.0 18.4 - - + -
666A LEU* 4.1 15.6 - - + +
668A LEU* 3.9 21.8 - - + -
711A MET 3.0 12.3 + - - +
712A LYS 3.5 9.6 - - - +
713A SER 3.1 0.4 - - - -
714A LEU* 1.3 75.0 - - - +
716A ARG* 1.3 70.5 + - + +
718A LEU* 2.9 16.4 + - - +
719A GLY 3.4 6.9 + - - -
720A CYS* 2.9 38.0 + - + +
722A PRO* 3.9 13.9 - - - +
725A LEU* 3.7 26.9 - - + +
728A LEU* 4.3 4.5 - - + -
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Residues in contact with ARG 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A ILE* 3.4 32.3 - - + +
640A ASP* 2.5 45.7 + - - -
712A LYS* 3.2 27.9 + - - +
713A SER* 3.1 11.7 + - - +
715A TYR* 1.3 87.5 - - + +
717A THR* 1.3 61.5 + - - +
718A LEU 3.3 0.7 + - - -
719A GLY* 3.3 13.9 + - - +
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Residues in contact with THR 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A ARG* 3.3 44.9 + - - +
713A SER* 3.1 22.8 + - - +
714A LEU* 2.7 14.2 + - + +
716A ARG* 1.3 77.5 - - + +
718A LEU* 1.3 63.8 + - - +
719A GLY* 4.5 0.6 - - - -
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Residues in contact with LEU 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A LEU* 3.7 37.2 - - + +
668A LEU* 3.8 20.6 - - + -
670A ARG* 5.2 2.8 + - - -
691A PHE* 3.6 53.1 - - + +
692A SER* 4.1 17.0 - - - +
693A ARG* 4.3 12.1 - - + +
714A LEU 3.8 8.1 - - - +
715A TYR 2.9 8.7 + - - +
717A THR* 1.3 84.4 + - - +
719A GLY* 1.3 63.8 + - - +
720A CYS* 3.2 4.1 + - - +
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Residues in contact with GLY 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ARG* 3.7 7.2 + - - -
715A TYR* 3.4 4.0 + - - -
716A ARG* 3.3 14.6 + - - -
717A THR 3.4 1.1 - - - -
718A LEU* 1.3 76.7 - - - +
720A CYS* 1.3 61.9 + - - +
721A PRO* 3.3 10.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il